Job ID = 10450969 sra ファイルのダウンロード中... Completed: 463181K bytes transferred in 14 seconds (265393K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 24357846 spots for /home/okishinya/chipatlas/results/dm3/SRX3404036/SRR6303513.sra Written 24357846 spots total rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:21:08 24357846 reads; of these: 24357846 (100.00%) were unpaired; of these: 771397 (3.17%) aligned 0 times 17475601 (71.75%) aligned exactly 1 time 6110848 (25.09%) aligned >1 times 96.83% overall alignment rate Time searching: 00:21:09 Overall time: 00:21:09 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3144779 / 23586449 = 0.1333 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Wed, 07 Feb 2018 14:17:37: # Command line: callpeak -t SRX3404036.bam -f BAM -g dm -n SRX3404036.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3404036.10 # format = BAM # ChIP-seq file = ['SRX3404036.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 07 Feb 2018 14:17:37: #1 read tag files... INFO @ Wed, 07 Feb 2018 14:17:37: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 14:17:37: # Command line: callpeak -t SRX3404036.bam -f BAM -g dm -n SRX3404036.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3404036.05 # format = BAM # ChIP-seq file = ['SRX3404036.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 07 Feb 2018 14:17:37: #1 read tag files... INFO @ Wed, 07 Feb 2018 14:17:37: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 14:17:37: # Command line: callpeak -t SRX3404036.bam -f BAM -g dm -n SRX3404036.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3404036.20 # format = BAM # ChIP-seq file = ['SRX3404036.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 07 Feb 2018 14:17:37: #1 read tag files... INFO @ Wed, 07 Feb 2018 14:17:37: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 14:17:47: 1000000 INFO @ Wed, 07 Feb 2018 14:17:47: 1000000 INFO @ Wed, 07 Feb 2018 14:17:48: 1000000 INFO @ Wed, 07 Feb 2018 14:17:56: 2000000 INFO @ Wed, 07 Feb 2018 14:17:56: 2000000 INFO @ Wed, 07 Feb 2018 14:17:56: 2000000 INFO @ Wed, 07 Feb 2018 14:18:04: 3000000 INFO @ Wed, 07 Feb 2018 14:18:05: 3000000 INFO @ Wed, 07 Feb 2018 14:18:05: 3000000 INFO @ Wed, 07 Feb 2018 14:18:12: 4000000 INFO @ Wed, 07 Feb 2018 14:18:13: 4000000 INFO @ Wed, 07 Feb 2018 14:18:14: 4000000 INFO @ Wed, 07 Feb 2018 14:18:20: 5000000 INFO @ Wed, 07 Feb 2018 14:18:22: 5000000 INFO @ Wed, 07 Feb 2018 14:18:23: 5000000 INFO @ Wed, 07 Feb 2018 14:18:28: 6000000 INFO @ Wed, 07 Feb 2018 14:18:30: 6000000 INFO @ Wed, 07 Feb 2018 14:18:31: 6000000 INFO @ Wed, 07 Feb 2018 14:18:36: 7000000 INFO @ Wed, 07 Feb 2018 14:18:39: 7000000 INFO @ Wed, 07 Feb 2018 14:18:40: 7000000 INFO @ Wed, 07 Feb 2018 14:18:43: 8000000 INFO @ Wed, 07 Feb 2018 14:18:47: 8000000 INFO @ Wed, 07 Feb 2018 14:18:48: 8000000 INFO @ Wed, 07 Feb 2018 14:18:52: 9000000 INFO @ Wed, 07 Feb 2018 14:18:55: 9000000 INFO @ Wed, 07 Feb 2018 14:18:57: 9000000 INFO @ Wed, 07 Feb 2018 14:19:00: 10000000 INFO @ Wed, 07 Feb 2018 14:19:03: 10000000 INFO @ Wed, 07 Feb 2018 14:19:05: 10000000 INFO @ Wed, 07 Feb 2018 14:19:08: 11000000 INFO @ Wed, 07 Feb 2018 14:19:11: 11000000 INFO @ Wed, 07 Feb 2018 14:19:13: 11000000 INFO @ Wed, 07 Feb 2018 14:19:16: 12000000 INFO @ Wed, 07 Feb 2018 14:19:20: 12000000 INFO @ Wed, 07 Feb 2018 14:19:22: 12000000 INFO @ Wed, 07 Feb 2018 14:19:24: 13000000 INFO @ Wed, 07 Feb 2018 14:19:28: 13000000 INFO @ Wed, 07 Feb 2018 14:19:30: 13000000 INFO @ Wed, 07 Feb 2018 14:19:32: 14000000 INFO @ Wed, 07 Feb 2018 14:19:36: 14000000 INFO @ Wed, 07 Feb 2018 14:19:38: 14000000 INFO @ Wed, 07 Feb 2018 14:19:40: 15000000 INFO @ Wed, 07 Feb 2018 14:19:44: 15000000 INFO @ Wed, 07 Feb 2018 14:19:47: 15000000 INFO @ Wed, 07 Feb 2018 14:19:48: 16000000 INFO @ Wed, 07 Feb 2018 14:19:52: 16000000 INFO @ Wed, 07 Feb 2018 14:19:55: 16000000 INFO @ Wed, 07 Feb 2018 14:19:56: 17000000 INFO @ Wed, 07 Feb 2018 14:20:01: 17000000 INFO @ Wed, 07 Feb 2018 14:20:03: 17000000 INFO @ Wed, 07 Feb 2018 14:20:04: 18000000 INFO @ Wed, 07 Feb 2018 14:20:09: 18000000 INFO @ Wed, 07 Feb 2018 14:20:11: 18000000 INFO @ Wed, 07 Feb 2018 14:20:12: 19000000 INFO @ Wed, 07 Feb 2018 14:20:18: 19000000 INFO @ Wed, 07 Feb 2018 14:20:19: 19000000 INFO @ Wed, 07 Feb 2018 14:20:20: 20000000 INFO @ Wed, 07 Feb 2018 14:20:25: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 14:20:25: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 14:20:25: #1 total tags in treatment: 20441670 INFO @ Wed, 07 Feb 2018 14:20:25: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 14:20:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 14:20:25: #1 tags after filtering in treatment: 20441670 INFO @ Wed, 07 Feb 2018 14:20:25: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 14:20:25: #1 finished! INFO @ Wed, 07 Feb 2018 14:20:25: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 14:20:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 14:20:27: #2 number of paired peaks: 298 WARNING @ Wed, 07 Feb 2018 14:20:27: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Wed, 07 Feb 2018 14:20:27: start model_add_line... INFO @ Wed, 07 Feb 2018 14:20:28: start X-correlation... INFO @ Wed, 07 Feb 2018 14:20:28: end of X-cor INFO @ Wed, 07 Feb 2018 14:20:28: #2 finished! INFO @ Wed, 07 Feb 2018 14:20:28: #2 predicted fragment length is 86 bps INFO @ Wed, 07 Feb 2018 14:20:28: #2 alternative fragment length(s) may be 4,86 bps INFO @ Wed, 07 Feb 2018 14:20:28: #2.2 Generate R script for model : SRX3404036.05_model.r WARNING @ Wed, 07 Feb 2018 14:20:28: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 14:20:28: #2 You may need to consider one of the other alternative d(s): 4,86 WARNING @ Wed, 07 Feb 2018 14:20:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 07 Feb 2018 14:20:28: #3 Call peaks... INFO @ Wed, 07 Feb 2018 14:20:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 14:20:28: 20000000 INFO @ Wed, 07 Feb 2018 14:20:28: 20000000 INFO @ Wed, 07 Feb 2018 14:20:32: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 14:20:32: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 14:20:32: #1 total tags in treatment: 20441670 INFO @ Wed, 07 Feb 2018 14:20:32: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 14:20:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 14:20:32: #1 tags after filtering in treatment: 20441670 INFO @ Wed, 07 Feb 2018 14:20:32: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 14:20:32: #1 finished! INFO @ Wed, 07 Feb 2018 14:20:32: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 14:20:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 14:20:32: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 14:20:32: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 14:20:32: #1 total tags in treatment: 20441670 INFO @ Wed, 07 Feb 2018 14:20:32: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 14:20:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 14:20:33: #1 tags after filtering in treatment: 20441670 INFO @ Wed, 07 Feb 2018 14:20:33: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 14:20:33: #1 finished! INFO @ Wed, 07 Feb 2018 14:20:33: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 14:20:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 14:20:34: #2 number of paired peaks: 298 WARNING @ Wed, 07 Feb 2018 14:20:34: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Wed, 07 Feb 2018 14:20:34: start model_add_line... INFO @ Wed, 07 Feb 2018 14:20:34: start X-correlation... INFO @ Wed, 07 Feb 2018 14:20:34: end of X-cor INFO @ Wed, 07 Feb 2018 14:20:34: #2 finished! INFO @ Wed, 07 Feb 2018 14:20:34: #2 predicted fragment length is 86 bps INFO @ Wed, 07 Feb 2018 14:20:34: #2 alternative fragment length(s) may be 4,86 bps INFO @ Wed, 07 Feb 2018 14:20:34: #2.2 Generate R script for model : SRX3404036.20_model.r WARNING @ Wed, 07 Feb 2018 14:20:34: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 14:20:34: #2 You may need to consider one of the other alternative d(s): 4,86 WARNING @ Wed, 07 Feb 2018 14:20:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 07 Feb 2018 14:20:34: #3 Call peaks... INFO @ Wed, 07 Feb 2018 14:20:34: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 14:20:35: #2 number of paired peaks: 298 WARNING @ Wed, 07 Feb 2018 14:20:35: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Wed, 07 Feb 2018 14:20:35: start model_add_line... INFO @ Wed, 07 Feb 2018 14:20:35: start X-correlation... INFO @ Wed, 07 Feb 2018 14:20:35: end of X-cor INFO @ Wed, 07 Feb 2018 14:20:35: #2 finished! INFO @ Wed, 07 Feb 2018 14:20:35: #2 predicted fragment length is 86 bps INFO @ Wed, 07 Feb 2018 14:20:35: #2 alternative fragment length(s) may be 4,86 bps INFO @ Wed, 07 Feb 2018 14:20:35: #2.2 Generate R script for model : SRX3404036.10_model.r WARNING @ Wed, 07 Feb 2018 14:20:35: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 14:20:35: #2 You may need to consider one of the other alternative d(s): 4,86 WARNING @ Wed, 07 Feb 2018 14:20:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 07 Feb 2018 14:20:35: #3 Call peaks... INFO @ Wed, 07 Feb 2018 14:20:35: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 14:21:22: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 14:21:29: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 14:21:31: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 14:21:52: #4 Write output xls file... SRX3404036.05_peaks.xls INFO @ Wed, 07 Feb 2018 14:21:52: #4 Write peak in narrowPeak format file... SRX3404036.05_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 14:21:52: #4 Write summits bed file... SRX3404036.05_summits.bed INFO @ Wed, 07 Feb 2018 14:21:52: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (12976 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 14:22:03: #4 Write output xls file... SRX3404036.10_peaks.xls INFO @ Wed, 07 Feb 2018 14:22:03: #4 Write peak in narrowPeak format file... SRX3404036.10_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 14:22:03: #4 Write summits bed file... SRX3404036.10_summits.bed INFO @ Wed, 07 Feb 2018 14:22:03: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3200 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 14:22:04: #4 Write output xls file... SRX3404036.20_peaks.xls INFO @ Wed, 07 Feb 2018 14:22:04: #4 Write peak in narrowPeak format file... SRX3404036.20_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 14:22:04: #4 Write summits bed file... SRX3404036.20_summits.bed INFO @ Wed, 07 Feb 2018 14:22:04: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1244 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。